Re: [gmx-users] Issues using tabulated potentials for coarse-grained simulation
Hi Tamrisa, Sorry for the slow response. Was a bit busy this weekend. I'm guessing you are using Bhargava and Klein's model? I made a mistake in setting the number of exclusions to 3 rather than 2 for their model. After I made that change, things ended up working out. If you are using the SDK water model, I should mention I also had some issues of the water freezing depending on how I set my initial conditions. Annealing the system resolved that issue (~400 K for a few ns). Hope this helps! Regards, Brian On Saturday, July 25, 2015, Tamisra Pal tamisra1...@gmail.com wrote: Hi Brian : I am also having a similar kind of issue in running a simulation of CG model Ionic liquid molecules having tabulated 9-6 LJ potential . Surprisingly , I find that the density steadily increasing even after 30 ns , and the box length consequently decreasing . Though the temperature , pressure are OK . In my case I have used tc-grps = system . Can you tell me how to resolve this issue ? Are there any other techniques without using separate temperature couplings for group molecules? Thanks Tamisra -- -- Tamisra Pal Post Doctoral Research Fellow Technische Universität Darmstadt Institut für Festkörperphysik Hochschulstraße 6 64289 Darmstadt , Germany -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org javascript:;. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Umbrella Sampling - no PMF plateau
Hi Steven, I've run into a similar issue with CG simulations using tabulated potentials. For my system it turns out the continuous increase in PMF was due to the system freezing for some unknown reason. Once I annealed the system (~500 K) and messed around with the temperature coupling, the system unfroze, and I was eventually able to obtain the correct plateau in the PMF curve. Have you checked some of your configurations to see whether your system shows unphysical ordering? (I am assuming you are using an explicit solvent.) Hope this helps, Brian On Tue, Aug 5, 2014 at 5:19 AM, Steven Neumann s.neuman...@gmail.com wrote: Dear Gmx Users, I run US simulations between 2 nanotubes with attached proteins with distance as a reaction coordinate. This is a coarse-grain simulation, both tubes are placed across pbc so infinite in length. I have tabulated potentials for both bonded and non-bonded interactions. I observed that even at large distances between them in US windows when they do not interact (even across pbc) the PMF is still increasing... no plateau is observed... I tried it in many systems increasing the box size but still the same happening. The perido image is 15 nm away and the cutoff in potentials is 2 nm... Would you please advise? May that correspond to position restraint dynamics of tube atoms of one of them (from which I pulled the other one)? Or maybe tabulated potentials used? Steven -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Issues using tabulated potentials for coarse-grained simulation
Thanks for the response. I have looked at two particles in NVT with v-rescale/large box and there was nothing wrong with the intra/inter molecular interaction energies. I also switched rvdw-switch to rvdw without observing any difference. I ran into a similar issue when using this force field in a system containing a mixture. I was able to resolve the issue again, though this time with annealing and varying the temperature coupling groups. Perhaps this only happens when there are more degrees of freedom and a greater likelihood for metastability (?). I will just be a bit more cautious from this point on when running these CG simulations. Thanks again, Brian On Wed, Jul 23, 2014 at 4:09 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, All sounds very weird. I would be suspicious of the fact that you haven't set rvdw. I have no idea what rvdw-switch might do in this context, but I definitely think you should verify that systems with just two particles have the interaction strength you can compute manually. Mark On Mon, Jul 21, 2014 at 8:57 PM, Brian Yoo brian.s.yoo...@nd.edu wrote: Dear gmx-users, I am running into an issue regarding the use of tabulated potentials for coarse-grained simulations. My system consists of 256 ion pairs (ionic liquid) and the simulation is run in the NPT ensemble. When I use a temperature coupling on the system as a whole, my system ends up freezing such that the ions vibrate in position. The temperatures and pressures are correct, but the density is much higher than what it should be. Also, the system is stable and the simulation runs indefinitely. However, if I set temperature coupling of anions and cations separately, my molecules no longer freeze and I obtain the targeted properties almost exactly. This occurrence is insensitive to varying tau-t's (0.5 to 5.0) or thermostat (Berendsen or Nose-Hoover), and annealing. It also occurs for other systems using a similar ionic liquid force field, although I was able to resolve the issue again by changing the temperature coupling to anions and cations separately. I have not run into this type of issue for all atom simulations of ionic liquids. The force field is based on a 9-6 Mie cutoff potential and PME long-range electrostatics. Has anyone run into a similar issue using tabulated potentials? Thank you, Brian Yoo The mdp parameters are as follows: integrator = md dt = 0.004 nsteps = 500 comm-mode = linear nstcomm = 1 ; Output control nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 5000 nstxtcout = 5000 ; Neighbor searching nstlist = 10 ns_type = grid pbc = xyz rlist = 1.5 ;Electrostatics coulombtype = PME rcoulomb= 1.5 fourierspacing = 0.10 optimize_fft= yes ; VdW vdwtype = user rvdw-switch = 1.5 ; Temperature coupling tcoupl = Berendsen tc-grps = C4M PF; System tau_t = 0.5 0.5 ref_t = 300 300 ; Pressure coupling pcoupl = Berendsen pcoupltype = isotropic ref_p = 1.0 tau_p = 3.0 compressibility = 4.5e-5 ; Velocity generation gen_vel = yes continuation= no -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Issues using tabulated potentials for coarse-grained simulation
Dear gmx-users, I am running into an issue regarding the use of tabulated potentials for coarse-grained simulations. My system consists of 256 ion pairs (ionic liquid) and the simulation is run in the NPT ensemble. When I use a temperature coupling on the system as a whole, my system ends up freezing such that the ions vibrate in position. The temperatures and pressures are correct, but the density is much higher than what it should be. Also, the system is stable and the simulation runs indefinitely. However, if I set temperature coupling of anions and cations separately, my molecules no longer freeze and I obtain the targeted properties almost exactly. This occurrence is insensitive to varying tau-t's (0.5 to 5.0) or thermostat (Berendsen or Nose-Hoover), and annealing. It also occurs for other systems using a similar ionic liquid force field, although I was able to resolve the issue again by changing the temperature coupling to anions and cations separately. I have not run into this type of issue for all atom simulations of ionic liquids. The force field is based on a 9-6 Mie cutoff potential and PME long-range electrostatics. Has anyone run into a similar issue using tabulated potentials? Thank you, Brian Yoo The mdp parameters are as follows: integrator = md dt = 0.004 nsteps = 500 comm-mode = linear nstcomm = 1 ; Output control nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 5000 nstxtcout = 5000 ; Neighbor searching nstlist = 10 ns_type = grid pbc = xyz rlist = 1.5 ;Electrostatics coulombtype = PME rcoulomb= 1.5 fourierspacing = 0.10 optimize_fft= yes ; VdW vdwtype = user rvdw-switch = 1.5 ; Temperature coupling tcoupl = Berendsen tc-grps = C4M PF; System tau_t = 0.5 0.5 ref_t = 300 300 ; Pressure coupling pcoupl = Berendsen pcoupltype = isotropic ref_p = 1.0 tau_p = 3.0 compressibility = 4.5e-5 ; Velocity generation gen_vel = yes continuation= no -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
